17-44148179-A-C

Variant names:

• chr17-44148179-A-C
• rs227584
• NM_001171251.3:c.376A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001171251.3(HROB):​c.376A>C​(p.Thr126Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 1,613,906 control chromosomes in the GnomAD database, including 112,733 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.48 (21461 hom., cov: 32)
  • Exomes 𝑓: 0.33 (91272 hom.)
• Consequence: HROB NM_001171251.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126
• Publications: 94 publications found

Genes affected

HROB (HGNC:28460): (homologous recombination factor with OB-fold) Predicted to enable single-stranded DNA binding activity. Involved in DNA synthesis involved in DNA repair and interstrand cross-link repair. Located in site of DNA damage. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=1.1212045E-6).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.806 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001171251.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HROB	NM_001171251.3	MANE Select	c.376A>C	p.Thr126Pro	missense	Exon 3 of 10	NP_001164722.1
	HROB	NM_024032.5		c.376A>C	p.Thr126Pro	missense	Exon 3 of 10	NP_076937.2
	HROB	NM_001321311.2		c.376A>C	p.Thr126Pro	missense	Exon 3 of 10	NP_001308240.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HROB	ENST00000585683.6	TSL:2 MANE Select	c.376A>C	p.Thr126Pro	missense	Exon 3 of 10	ENSP00000466618.1
	HROB	ENST00000319977.8	TSL:1	c.376A>C	p.Thr126Pro	missense	Exon 3 of 10	ENSP00000313500.4
	HROB	ENST00000245382.6	TSL:1	c.376A>C	p.Thr126Pro	missense	Exon 3 of 7	ENSP00000245382.5

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72975 AN: 151902 Hom.: 21401 Cov.: 32

Gnomad AFR AF: 0.813

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.435

GnomAD2 exomes AF: 0.401 AC: 100882 AN: 251326 AF XY: 0.381

Gnomad AFR exome AF: 0.823

Gnomad AMR exome AF: 0.454

Gnomad ASJ exome AF: 0.483

Gnomad EAS exome AF: 0.787

Gnomad FIN exome AF: 0.322

Gnomad NFE exome AF: 0.302

Gnomad OTH exome AF: 0.376

GnomAD4 exome AF: 0.334 AC: 488486 AN: 1461886 Hom.: 91272 Cov.: 60 AF XY: 0.331 AC XY: 240596 AN XY: 727246

African (AFR) AF: 0.830 AC: 27777 AN: 33480

American (AMR) AF: 0.456 AC: 20377 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.482 AC: 12592 AN: 26136

East Asian (EAS) AF: 0.744 AC: 29531 AN: 39700

South Asian (SAS) AF: 0.291 AC: 25073 AN: 86258

European-Finnish (FIN) AF: 0.320 AC: 17078 AN: 53418

Middle Eastern (MID) AF: 0.358 AC: 2063 AN: 5768

European-Non Finnish (NFE) AF: 0.297 AC: 330685 AN: 1112006

Other (OTH) AF: 0.386 AC: 23310 AN: 60396

GnomAD4 genome AF: 0.481 AC: 73099 AN: 152020 Hom.: 21461 Cov.: 32 AF XY: 0.479 AC XY: 35624 AN XY: 74298

African (AFR) AF: 0.814 AC: 33749 AN: 41478

American (AMR) AF: 0.452 AC: 6894 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.487 AC: 1691 AN: 3470

East Asian (EAS) AF: 0.776 AC: 4010 AN: 5170

South Asian (SAS) AF: 0.307 AC: 1478 AN: 4820

European-Finnish (FIN) AF: 0.315 AC: 3329 AN: 10558

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.304 AC: 20671 AN: 67942

Other (OTH) AF: 0.434 AC: 917 AN: 2114

Alfa AF: 0.376 Hom.: 54831

Bravo AF: 0.513

TwinsUK AF: 0.293 AC: 1085

ALSPAC AF: 0.285 AC: 1099

ESP6500AA AF: 0.794 AC: 3497

ESP6500EA AF: 0.310 AC: 2666

ExAC AF: 0.402 AC: 48809

Asia WGS AF: 0.533 AC: 1856 AN: 3478

EpiCase AF: 0.300

EpiControl AF: 0.303

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.044
BayesDel_addAF	Benign	-0.77	T
BayesDel_noAF	Benign	-0.74
CADD	Benign	4.3
DANN	Benign	0.10
DEOGEN2	Benign	0.0015	T
Eigen	Benign	-1.4
Eigen_PC	Benign	-1.3
FATHMM_MKL	Benign	0.0086	N
LIST_S2	Benign	0.14	T
MetaRNN	Benign	0.0000011	T
MetaSVM	Benign	-0.99	T
MutationAssessor	Benign	-1.8	N
PhyloP100		-0.13
PROVEAN	Benign	2.2	N
REVEL	Benign	0.070
Sift	Benign	1.0	T
Sift4G	Benign	0.64	T
Polyphen		0.0	B
Vest4		0.033
MPC		0.16
ClinPred		0.0019	T
GERP RS		1.5
Varity_R		0.050
gMVP		0.051
Mutation Taster		=97/3	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs227584; hg19: chr17-42225547; COSMIC: COSV55370618;